---
title: "Report"
output: 
    flexdashboard::flex_dashboard:
        source_code: embed
        vertical_layout: scroll
---

```{r}
# Function to plot 3D UMAP with selected feature
umap_feature <- function(feature) {

    metadata <- colnames(seurat[[]])
    if (feature %in% c(metadata, rownames(seurat))) {

        color_counts <- as.vector(seurat[["RNA"]][feature, ])
        p <- plot_ly(type = "scatter3d", x = umap_emb[, 1], y = umap_emb[, 2], z = umap_emb[, 3],
                     mode = "markers", color = color_counts, colors = pal(20), size = 1)

    } else {
        par(mar = c(0,0,0,0))
        p <- plot(c(0, 1), c(0, 1), ann = F, bty = 'n', type = 'n', xaxt = 'n', yaxt = 'n')  +
            text(x = 0.5, y = 0.5, paste0("Feature not found: ", feat), cex = 1.6, col = "black")

}
    return(p)
}
```

Column 
-------------------------------------

### Cluster

```{r}
umap_cluster <- plot_ly(type = "scatter3d", x = umap_emb[, 1], y = umap_emb[, 2], z = umap_emb[, 3], mode = "markers", color = seurat$seurat_clusters, text = seurat$seurat_clusters, size = 1)
umap_cluster
```

### OPCs - PTPRZ1

```{r}
# PTPRZ1
feat <- "PTPRZ1"
umap_feature(feat)
```

### Oligos - Olig1

```{r}
feat <- "OLIG1"
umap_feature(feat)
```

Column
---------------------------------

### Total UMI

```{r}
# Total UMI
feat <- "nCount_RNA"
cols <- brewer.pal(8, "OrRd")
pal <- colorRampPalette(cols)
color_feat <- seurat[[feat]][[1]]
umap_ntotal <- plot_ly(type = "scatter3d", x = umap_emb[, 1], y = umap_emb[, 2], z = umap_emb[, 3], mode = "markers", color = color_feat, colors = pal(20), size = 1)
umap_ntotal
```

### OPCs - PDGFRA

```{r}
feat <- "PDGFRA"
umap_feature(feat)
```

### Oligos - Olig2

```{r}
feat <- "OLIG2"
umap_feature(feat)
```

Column
---------------------------------

### Total features

```{r}
# Total features
feat <- "nFeature_RNA"
cols <- brewer.pal(8, "OrRd")
pal <- colorRampPalette(cols)
color_feat <- seurat[[feat]][[1]]
umap_nfeats <- plot_ly(type = "scatter3d", x = umap_emb[, 1], y = umap_emb[, 2], z = umap_emb[, 3], mode = "markers", color = color_feat, colors = pal(20), size = 1)
umap_nfeats
```

### OPCs - SOX2

```{r}
feat <- "SOX2"
umap_feature(feat)
```

### Oligos - GLAST

```{r}
feat <- "GLAST"
umap_feature(feat)
```